On BioScience and Life and Such

Posts Tagged ‘science’

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Publication phusis, Call for help

In Uncategorized on June 16, 2008 at 11:10 am

I have had many thoughts on how to present scientific data, and will have many more. SciPhu is, so far, the compilation of some of those, and blogging is the adverse event from trying to realize them. I have however come as far as I can on my own and need help to carry this project through.

This is what I have been planning: SciPhu is supposed to develop into a certification site for scientific thoughts, ideas and data. It is supposed to gather a large community of competent reviewers from virtually any scientific field. These reviewers are supposed to provide thorough peer-reviews of any scientific presentation as requested for evaluation on SciPhu.com. A successful review is supposed to give the author(s) a stamp to put on their presentation as a guarantee for scientific quality and credibility.

Through a FriendFeed discussion (original post by Bill Hooker) I came across this commentary on the problems of evaluating online publications. The author, Gary A. Olson, presents some solutions that are very similar to the principles I’ve worked out for Sciphu.

Clearly, the scholarly community needs to devise a way to introduce dependability into the world of electronic scholarship. We need a process to certify sites so that we all can distinguish between one that contains reliable material and one that may have been slapped together by a dilettante. We need to be able to ascertain if we can rely on a site for our own scholarship and whether we should give credit toward a colleague’s tenure and promotion for a given site.

And he proposes to establish certification bodies to achieve these goals.

The major professional and scholarly organizations in each discipline should (devise a certification process in which a site owner can apply to have a site reviewed and recognized, perhaps for a nominal processing fee. The site would be subjected to a formal and rigorous review by peers in the disciplinary area covered by the site.

Which is a very good description of what I wanted SciPhu to be like (except for maybe the fee, which should be for commercial users only). I have taken the liberty to replace with SciPhu in relevant places in the rest of these bullet points (the original text in brackets):

  • Only those sites meeting the highest standards should be awarded certification.
  • Once a site wins certification from SciPhu (the national scholarly society), it should be permitted to display that stamp of approval prominently.
  • The certification should remain in effect for a specific and limited amount of time (since a site can change rapidly and without notice). The site should regularly seek renewal of its certification.
  • SciPhu (Each disciplinary organization) should issue a resolution recommending that departments construe certification of a site as indicating that it has met the highest standards of scholarship.
  • SciPhu (Each organization) should maintain an online registry of certified sites.

A central site accessible to all is much more efficient than local evaluation bodies. Also the potential to gather a large collection of qualified referees is present only on a truly international site. Such a broad site would also be able to satisfy the open-access requirements in our Web/Science 2.0 future.

The SciPhu blog was set up as a starting point to gather a community of peer-reviewers. Making the blog successful is going to take a long time however, and given this commentary as well as the current interest in different publishing models, it seems wise to try and speed up.

To do this I need help. I need help setting up a good site, – a wiki perhaps. I also need help advertising this to the broader Scientific community and recruit referees. Even with help, achieving success is not going to be a stroll in the park. But without help it is going to be near impossible.

The end result may not end up as originally planned: names, concepts and strategies may/will change on the way, but I strongly believe that this is a path worth traveling.

I also think that Gary A. Olson is to narrowminded when it comes to requirements and scope of such a certification. Doing this online with a large community of referees makes it possible to get peer-review very quickly because reviewers would be accessible around the world 24-7. And there is no reason to limit such reviews to scientific publications. Any news-piece, advertisement or company information with scientific content could get reviewing through a SciPhu-like site. Extending reviewing to non-scientific publication forums is also the commercial opportunity, or business model if you will.

If you are interested in starting a broad and open-minded collaboration on this (and I really hope you are), please leave a comment, send me a mail or even better, join and use The Life Scientists room on FriendFeed for further discussions.

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And now suddenly, we don’t need genetic counselors anymore…..?

In Uncategorized on May 30, 2008 at 12:16 pm

With this post, my posts on genetic counseling are now a trilogy (which somewhat unfairly puts them in the same category as some amazing literature, – and films).

From a recent Nature News Special Report:

No one denies that genetic test results can be life-altering for some individuals. But research by Theresa Marteau, a health psychologist at King’s College London, and others has shown that most people are remarkably resilient in the face of traumatic genetic test results. They typically report feeling anxious or depressed around the time of testing, but these effects dwindle within a few months.

This fits well with my first post where I argued that the need for genetic counselors was overrated. After reading an article on Huntington’s disease however, I changed my mind, and wrote another blog post. But now, this quote contradicts what I thought was my final conclusions and I am left wondering where I stand … again:

Studies by Aad Tibben, a psychologist and psychotherapist at Leiden University Medical Centre in the Netherlands, and his colleagues showed that people who took predictive tests for Huntington’s disease mostly recovered from the shock. Many actually felt more in control after testing because they could make arrangements for care, or even for euthanasia.

And I am not the only one who is confused on these matters

With so much uncertainty about how people deal with genetic risk, is genetic counselling necessary or helpful for people undergoing the less definitive tests for an increased propensity for heart conditions or diabetes? “I’m convinced it’s necessary,” says Tibben. But he and others in the field acknowledge that there is little in the way of controlled trials to support their belief.

I have decided to go with the conclusion that the best thing to do is probably to do the genetic counseling,… and then evaluate,… and then stop doing it if it doesn’t work. This simply because to my knowledge, genetic counseling doesn’t do any harm. It may even do some good even if the effect is all placebo:

“……….Did the counsellor help the patient understand complicated risks, or just provide some face-to-face contact and empathy in a confusing medical world?

So, until someone comes out with a study that says that genetic counseling is harmful, this post will reflect my final (!?) postition. End of story (trilogy).

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How everything is a mess and still ok

In Uncategorized on May 26, 2008 at 9:09 am


post to news.thinkgene.com

I have recently finished reading a Nature news feature on noise in gene expression (The Cellular Hullabaloo). It left me with this increased understanding of cellular processes and in terms of controlling chaos, fitted nicely with something I have blogged about before, which is Hsp’s (especially Hsp90).

According to this news feature, several studies have found that there are significant differences in the expression of genes both in duration and strength, even between cells that were expected to be identical. This contradicts the current notion of gene expression as an orderly sequential and structured phenomenon. These studies seem to indicate that gene expression occurs randomly, throughout the whole genome.

How these cells are still able to differentiate in a predictable manner,…… and perform specialized functions in concert with thousands of other cells,…….. to build a functional multicellular organism, is a mystery to me. And it is enigmatic to the researchers behind these studies as well:

“People are fascinated by how we do what we do despite this noise.” — James Collins

and

“People ask how come an organism works so well. Perhaps it doesn’t work so well. Perhaps organisms without these fluctuations would outcompete us.” – Johan Paulsson

How the noise came about and why it persists is still somewhat unclear, but benefits from such chaotic conditions may arise from:

1. Controlling randomness (noise) requires a lot of energy, the more chaos the less energy spent. Consequently, only the most critical cellular processes are under tight control, and the rest are more or less random.

2. Expression noise may enable cells to fight off threats. Say a certain level of protein is required to survive a toxic compound attack. Then having cells with sufficient levels of defender protein is more probable in a (noisy) cell population with varying gene expression levels, than in cell populations with a constant level of expression.

3. Randomness may ensure variation in differentiation. An example given in the news feature is the differentiation of blue and green light sensing photoreceptors in drosophila.

So, the noise is there for a reason. Noise, or more precisely – random fluctuation, is an ubiquitous cellular phenomenon. But cells of a given type still end up with similar morphology and similar functionality. The beauty of nature is how the randomness is controlled just enough to achieve the minimum amount of order necessary for preserving functionality. Also, in keeping the random events, flexibility is preserved for future adaptation.

The chaos extends further than gene-expression. If you also consider variations in insertions/deletions, gene copy number and epigenetic differences, the potential for random variation at the gene level becomes evident. To control some of this genetic randomness you have proteins like Hsp90 that masks genetic variation at the transcription level (or folding level to be precise). This is an important control-mode for some of the chaos (DNA sequence variation and mutations) and at the same time it enables sudden exposure of chaos to achieve rapid morphological evolution if needed. I am pretty sure that similar (or very different) control mechanisms will be discovered for gene expression noise in the future.

The noisy expression story is another illustration of how we are not just our genes. The DNA-sequence may be a defining starting point, but there are levels and levels of variation on top of that. As multicellular and evolving organisms, we are constantly balancing between chaos and order. The chaos-level is maximized to minimize energy expenditure and to ensure a multitude of possible paths to follow in an organisms future biological evolution.

The balance is oh so beautiful, it’s called nature.

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Updated Normality

In Uncategorized on May 15, 2008 at 3:15 pm

Just to remind myself:

Something “Constant” exists only on paper or in silico.

In life “Normal” = Variation

Variation can be Random or have a Trend, but even the Trend Fluctuates and is never Constant.

If this is true then the terms “Constant” and “Life” are incompatible. And consequently, “Living a Normal Life” cannot possibly be Defined.

Updated from previous post “Normality“

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Now this is why we need genetic counselors

In Uncategorized on April 25, 2008 at 12:00 pm

After reading “Living at risk: Concealing risk and Preserving Hope“, which was an eye-opening experience, I am ready to argue against myself and the arguments in my previous post “Now why do we need genetic counselors ?”.

In this post I predicted that genetic counselors may soon be obsolete because nobody cares about low-risk alleles. In addition I argued that information on high-risk alleles is better managed by physicians.

The not caring bit is still true (unfortunately) as far as I know, but after reading the above mentioned paper, I need to modify my opinion on high risk tests. High risk tests in this context, are tests that if positive, means developing disease in the near future. Testing for Huntington disease is a model example of such tests since:

“Penetrance, the likelihood of showing symptoms of the disease if the associated genetic mutation is present, is virtually 100%.”

Thus, this is a clear medical case and a physician should be able to give adequate counsel to the patient. But, the issues a practitioner would face are so much more than medicine alone and recommendations for counseling goes wider than what is expected of a primary care physician:

Nearly every participant with children experienced terrible difficulty in talking to their children about their risk, even when the children were grown. We infer from this difficulty that practitioners could, and should, find ways to help people at risk develop plans for educating their children at an appropriate age. We envision such plans to be developmentally based, geared to answering questions at the child’s level, as well as being persistent and gradual in the presentation of the issues of importance.

This to me, sounds like genetic counseling. Further arguments for genetic counseling comes from the recommendations to the clinicians:

Clinicians also need to reflect on their own beliefs and biases about genetic testing, and to examine the extent to which those beliefs and biases present themselves in their care for people at risk for HD. Primary care health professionals need to be cognizant of the fact that just because a test can be done does not mean that it should be done. What these men and women are telling us is that it is not safe to assume that genetic testing for incurable diseases will necessarily provide information that is wanted, or needed, by those at risk and that testing may have a significant negative impact on the lives of their patients.

Objectively reflecting on genetic testing as well as telling the patient that it may actually be wise not to get tested, are probably things a genetic counselor would do better than the primary care physician.

So, the conclusion must be: I was wrong, we need genetic counselors. Reading “Living at risk: Concealing risk and Preserving Hope” will tell you this. In adition it will teach you that 80-85 % of at risk individuals elects not to undertake predictive genetic testing. They do so to survive since a lack of hope can be devastating:

Something that my uncle said, that I think really stuck with me, is he wrote a suicide note. He said that there’s such a big difference between living with hope and living with knowledge. And that he would take the living with hope any day. And so he really did not think we needed to know, one way or another.

…………and, proper counseling (not only genetic) may be a help for people in handling their life at risk since:

It is noteworthy that several participants said the interview for this study was their first opportunity to talk about the emotional side of HD, despite their years of experience with neurological, cognitive, and psychomotor testing …………… We think that unstructured interviews might actually change the views and actions of the participants with respect to their careful concealment of risk and their preservation of hope.

This is probably true. Regardless of the extent of counseling, it seems to me that genetic counseling for these patients and their family members is a good starting point.

The final take home message must be that not testing for a condition has significant value, especially when treatment options are scarce or non-existent.

Hope is sometimes a life saver. Knowledge on the other hand, can put peoples lives in ruins. Use this as a guiding light if you will, – I know I am going to.

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Now why do we need genetic counselors ?

In Uncategorized on April 17, 2008 at 11:49 am

According to the National Society of Genetic Counselors, genetic counseling is:

“the process of helping people understand and adapt to the medical, psychological and familial implications of genetic contributions to disease.”

But a commentary in Science Magazine indicates that these admirable goals are unachievable. It turns out that patients given genetic information on predisposition to disease don’t really care. Consequently, they are unlikely to do any changes to their lifestyle based on the test-results. Behavioral epidemiologist Colleen McBride and human geneticist Lawrence Brody are quoted saying:

“They’re not having big emotional
responses”

And subsequently the author concludes that:

“Behavioral specialists have shifted from
worrying about the devastating effects of
learning about these new genetic risks to
wondering whether the information will
make any impression at all.”

The REVEAL study (by way of Genomeboy) modifies the picture slightly on the willingness to change lifestyle based on test results from APOE, but confirms the lack of distress or anxiety resulting from test results. The REVEAL study was designed to measure:

  • Who seeks genetic counseling and why
  • How APOE disclosure affects risk perceptions
  • The psychological impact of genetic risk assessment
  • How risk information affects participants’ subsequent health and insurance behaviors.

Where the findings included:

  • Disclosing APOE status and its association with Alzheimer’s risk to participants did not result in a significant increase in distress or depression.
  • Participants who discovered they had the high risk APOE e4 allele proved more likely to be proactive in changing their lifestyles and planning for long term care.
  • A majority of participants reported that REVEAL had made a positive impact on their lives (67% positive vs. 17% negative).
  • Participants were more likely to report lower, rather than higher, anxiety about Alzheimer’s disease as a result of being tested (43% lower vs. 11% higher)

Thus, it seems the fear of damage caused by genetic test results is unwarranted or at least highly exaggerated. So, the question is: is there still a need for genetic counselors to ease distress ?

Yes one might answer, since genetic counseling is still needed to interpret the result. … – But,

In addition to the well known test for BRCA1, genetic tests are increasingly emerging that will give clear cut answers. Additional examples are colon cancer and lung cancer if you are a smoker. Understanding the technology behind the test becomes less important when test-results leads to unambiguous recommendations. No need to know what a SNP is if having it gives you a disease risk of 80-90 %. Thus, counseling to explain the problem of uncertain statistical probabilities may soon be obsolete.

If the risk turns out to be less than 80-90 % (and consequently less reliable for a physician as a proper pre-diagnostic test), according to the piece from Science magazine: it looks like nobody will care. If this is the case, genetic counseling for tests associated with medium to low risk becomes superfluous.

As an alternative then, I would suggest that genetic counselors turn their focus towards relieving group damages from genetic testing. That may be the life saver for a group of professionals once thought to have a bright future, now facing a dim/boring one.

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Richard Dawkins: an Evangelical atheist ?

In Uncategorized on April 14, 2008 at 1:07 pm

Something that should strike anyone reading, or listening to, Dawkins arguments against religion is: Being clever on hindsight is always easy.

Knowing what we know today, it is easy to see that God and religion are delusions (or faith as one might call it). Throughout history however, alternative explanations to existence has been sparse and religion has simply been the best explanation around. Consequently all known societies has had one or more Gods. Religion has been at the root of building society as we know it today, including the flaws.

Today, science builds society (including the flaws) more than religion does , – and increasingly so. Science is therefore at risk of becoming the new religion, and Dawkins may be destined for one of the new Archbishops. We should all learn from the history of religion and avoid the pitfall of discrediting and ridiculing what we cannot explain or things we currently cannot find supporting evidence for. What science cannot explain today, including any superhuman being or force, is not necessarily wrong for believers to believe in, – and who knows, evidence for some kind of a God may appear in the future when science has advanced further.

John Gray writes in “The Atheist delusion”

“Zealous atheism renews some of the worst features of Christianity and Islam. Just as much as these religions, it is a project of universal conversion. Evangelical atheists never doubt that human life can be transformed if everyone accepts their view of things, and they are certain that one way of living – their own, suitably embellished – is right for everybody. To be sure, atheism need not be a missionary creed of this kind. It is entirely reasonable to have no religious beliefs, and yet be friendly to religion. It is a funny sort of humanism that condemns an impulse that is peculiarly human. Yet that is what evangelical atheists do when they demonise religion.”

Instead of concluding the obvious (that God, as explained in the bible or elsewhere, is a delusion), we should take Dawkins’ writings as strong documentation for the continuing misuse of religion to oppress and abuse. The misuse is not caused by faith or religion in itself, but rather by people claiming religious leadership and authority. Their actions are probably more a result of darwinian principles (as the struggle to excede other members of a population, – through oppression or otherwise, is a fundamental darwinian principle), than they are results of religious faith.

This last point is important to remember because science will inevitably be misused the same way, and we as conscientious scientist are obliged to fight back.

This post is an update from the previous post: Richard Dawkins being clever on hindsight

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Launching SciPhu.com

In Uncategorized on April 7, 2008 at 12:55 pm

SciPhu= Science + Phusis

Phusis – An Ancient Greek word often translated as birth or nature (Wikipedia).

SciPhu.com is a blog based, open access and unrestricted publishing model. A hybrid in the spirit of Wikipedia and JustScience.

The idea behind SciPhu-publishing was to be able to publish and peer-review scientific information more efficiently than standard peer-reviewing. We wanted the reviewing process while retaining its scientific credibility, to be faster and less rigid. The answer, we found, is blogger-reviewing (which in this setting is just a fancy name for commenting on blog posts). Blogging is a good starting point since there are so many knowledgeable bloggers out there. While SciPhu may still be developed into a proper web-portal of some sort, the blog based starting point is now launched.

The end goal of SciPhu is to be able to quality control scientific information from any source, so that the twisted reality that sometimes ends up in the popular press (and ultimately in public opinion) can be promptly countered with proper accessible scientific information.

On the way towards this goal, we would like to provide a novel publishing channel for the scientific community. A way of publishing that is completely free of (any kind of) charge, less rigid, more efficient and more interactive than existing publishing models. SciPhu publishing is unlimited open-access and has the potential to reach a broad audience. At the same time, SciPhu aims be a pivotal tool to keep scientific authority intact, free and unpolitical.

Without input from (a lot of) you however, this effort will fail. Therefore, please feel free to contribute scientific content, recommend to friends and collegues or just come by to review/rate someone else’s work.

Invitation:

You are cordially invited to:

  • Write (blog) your own scientific article (or a review of a scientific topic).
  • Referee articles written by others.
  • Participate in scientific publishing in a new format.

You are invited to visit and join the SciPhu publishing community.


Clarifying Misuse of Science

In Uncategorized on December 17, 2007 at 2:53 pm

Just to expand a little on the subject, in our previous post, of misusing science. There are two ways of misusing (abusing ?) science. The first is twisting scientific facts to fit ones own agenda. The other and more immediate, way of misuse is achieved when ethics is left behind in practical applications of science. Prenatal testing for familial hypercholesterolemia is sad recent example of the latter.

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Richard Dawkins beeing clever on hindsight

In Uncategorized on December 14, 2007 at 10:14 am

Something that should strike anyone reading, or listening to, Dawkins arguments against religion is: Beeing clever on hindsight is always easy.

It is easy to see that God and religion are delusions (or faith as one might call it) knowing what we know today. Throughout history however, alternative explanations to existence has been sparse or non-existent and religion has been the best explanation anyone has been able to come up with. Consequently all known societies has had one or more Gods. Religion has been at the root of building society as we know it today, including the flaws.

Today, science builds society more than religion does, – and increasingly so. Science is therefore at risk of becoming the new religion, and Dawkins may be destined for one of the new Archbishops. We should all learn from the history of religion and avoid the pitfall of discrediting and ridiculing what we cannot explain or things we cannot find supporting evidence for. What science cannot explain today, including any superhuman beeing or force, is not necessarily wrong to believe in, and explanations or evidence for some kind of a God may appear in the future when scientific knowledge explains the currently hidden details.

Instead of concluding the obvious (that God is a delusion), we should take Dawkins arguments as strong documentation for the continuing misuse of religion to opress and abuse. This misuse is not due to faith in itself, but rather blaim should be put on the people claiming religious leadership and authority. These peoples actions are probably more a result of darwinian principles (as the struggle to excede other members of a population, – through oppression or otherwise, is a fundamental darwinian principle), than they are results of religious faith.

This last point is important to remember because science will inevitably be misused the same way, and we as scientist are obliged to fight back.